Identification of alpha-hemolytic streptococci by pyrosequencing the 16S rRNA gene and by use of VITEK 2

Journal of Clinical Microbiology

Volumn 45, Issue 3, 2007, Pages 762-770

  Haanperä, Marjo ^a   Jalava, Jari ^a   Huovinen, Pentti ^a   Meurman, Olli ^b   Rantakokko Jalava, Kaisu ^b  

^a NATIONAL PUBLIC HEALTH INSTITUTE   (Finland)

^b TURKU UNIVERSITY HOSPITAL   (Finland)

Author keywords

[No Author keywords available]

Indexed keywords

RNA 16S;

ALPHA HEMOLYTIC STREPTOCOCCUS; ANALYTIC METHOD; ARTICLE; BACTERIAL GENE; BACTERIAL STRAIN; BACTERIUM CULTURE; BACTERIUM IDENTIFICATION; BACTERIUM ISOLATION; GENE SEQUENCE; GENETIC VARIABILITY; GOLD STANDARD; NONHUMAN; NUCLEOTIDE SEQUENCE; PHENOTYPE; PRIORITY JOURNAL; STREPTOCOCCUS AGALACTIAE; STREPTOCOCCUS ANGINOSUS; STREPTOCOCCUS BOVIS; STREPTOCOCCUS CONSTELLATUS; STREPTOCOCCUS CRISTATUS; STREPTOCOCCUS DYSGALACTIAE; STREPTOCOCCUS EQUINUS; STREPTOCOCCUS GALLOLYTICUS; STREPTOCOCCUS GORDONII; STREPTOCOCCUS HYOINTESTINALIS; STREPTOCOCCUS INFANTARIUS; STREPTOCOCCUS INTERMEDIUS; STREPTOCOCCUS LUTETIENSIS; STREPTOCOCCUS MITIS; STREPTOCOCCUS ORALIS; STREPTOCOCCUS OVIS; STREPTOCOCCUS PARASANGUINIS; STREPTOCOCCUS PASTEURIANUS; STREPTOCOCCUS PHARYNGIS; STREPTOCOCCUS PNEUMONIAE; STREPTOCOCCUS PYOGENES; STREPTOCOCCUS SALIVARIUS; STREPTOCOCCUS SOBRINUS; STREPTOCOCCUS SUIS; STREPTOCOCCUS THORALTENSIS; STREPTOCOCCUS VESTIBULARIS; UNINDEXED SEQUENCE;

BACTERIAL TYPING TECHNIQUES; BACTERIOLOGICAL TECHNIQUES; BLOOD; DNA, BACTERIAL; GENES, RRNA; HUMANS; PHARYNX; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; STREPTOCOCCAL INFECTIONS; STREPTOCOCCUS;

STREPTOCOCCUS BOVIS; STREPTOCOCCUS PNEUMONIAE;

EID: 33947236210     PISSN: 00951137     EISSN: None     Source Type: Journal    
DOI: 10.1128/JCM.01342-06     Document Type: Article

References (37)

1. Bentley, R., and J. Leigh. 1995. Development of PCR-based hybridization protocol for identification of streptococcal species. J. Clin. Microbiol. 33: 1296-1301.
2. Bentley, R. W., J. A. Leigh, and M. D. Collins. 1991. Intrageneric structure of Streptococcus based on comparative analysis of small-subunit rRNA sequences. Int. J. Syst. Bacteriol. 41:487-494.
3. Bosshard, P. P., S. Abels, M. Altwegg, E. C. Bottger, and R. Zbinden. 2004. Comparison of conventional and molecular methods for identification of aerobic catalase-negative gram-positive cocci in the clinical laboratory. J. Clin. Microbiol. 42:2065-2073.
4. Clarridge, J. E., S. Attorri, D. M. Musher, J. Hebert, and S. Dunbar. 2001. Streptococcus intermedius, Streptococcus constellatus, and Streptococcus anginosus ("Streptococcus milleri group") are of different clinical importance and are not equally associated with abscess. Clin. Infect. Dis. 32:1511-1515.
5. Daley, P., D. L. Church, D. B. Gregson, and S. Elsayed. 2005. Species-level molecular identification of invasive "Streptococcus milleri" group clinical isolates by nucleic acid sequencing in a centralized regional microbiology laboratory. J. Clin. Microbiol. 43:2987-2988.
6. Drancourt, M., V. Roux, P.-E. Fournier, and D. Raoult. 2004. rpoB gene sequence-based identification of aerobic gram-positive cocci of the genera Streptococcus, Enterococcus, Gemella, Abiotrophia, and Granulicatella. J. Clin. Microbiol. 42:497-504.
7. Dwyer, R., and S. Ringertz. 1997. Viridans streptococci in blood cultures: can we see any patterns of species related to patient category? Review of 229 cases of positive cultures with viridans streptococci. APMIS 105:972-974.
8. Facklam, R. 2002. What happened to the streptococci: overview of taxonomic and nomenclature changes. Clin. Microbiol. Rev. 15:613-630.
9. Funke, G., and P. Funke-Kissling. 2005. Performance of the new VITEK 2 GP card for identification of medically relevant gram-positive cocci in a routine clinical laboratory. J. Clin. Microbiol. 43:84-88.
10. Garnier, F., G. Gerbaud, P. Courvalin, and M. Galimand. 1997. Identification of clinically relevant viridans group streptococci to the species level by PCR. J. Clin. Microbiol. 35:2337-2341.
11. Haanperä, M., P. Huovinen, and J. Jalava. 2005. Detection and quantification of macrolide resistance mutations at positions 2058 and 2059 of the 23S rRNA gene by pyrosequencing. Antimicrob. Agents Chemother. 49:457-460.
12. Hall, T. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp. Ser. 41:95-98.
13. Han, X. Y., M. Kamana, and K. V. I. Rolston. 2006. Viridans streptococci isolated by culture from blood of cancer patients: clinical and microbiologic analysis of 50 cases. J. Clin. Microbiol. 44:160-165.
14. Hoshino, T., T. Fujiwara, and M. Kilian. 2005. Use of phylogenetic and phenotypic analyses to identify nonhemolytic streptococci isolated from bacteremic patients. J. Clin. Microbiol. 43:6073-6085.
15. Innings, Å., M. Krabbe, M. Ullberg, and B. Herrmann. 2005. Identification of 43 Streptococcus species by pyrosequencing analysis of the mpB gene. J. Clin. Microbiol. 43:5983-5991.
16. Jacobs, J. A., H. C. Scheuten, E. E. Stobberingh, and P. B. Soeters. 1995. Viridans streptococci isolated from the bloodstream relevance of species identification. Diagn. Microbiol. Infect. Dis. 22:267-273.
17. Jalava, J., P. Kotilainen, S. Nikkari, M. Skurnik, E. Vänttinen, O. P. Lehtonen, E. Eerola, and P. Toivanen. 1995. Use of the polymerase chain reaction and DNA sequencing for detection of Bartonella quintana in the aortic valve of a patient with culture-negative infective endocarditis. Clin. Infect. Dis. 21:891-896.
18. Jonasson, J., M. Olofsson, and H.-J. Monstein. 2002. Classification, identification and subtyping of bacteria based on pyrosequencing and signature matching of 16S rDNA fragments. APMIS 110:263-272.
19. Kiratisin, P., L. Li, P. R. Murray, and S. H. Fischer. 2005. Use of housekeeping gene sequencing for species identification of viridans streptococci. Diagn. Microbiol. Infect. Dis. 51:297-301.
20. Li, Y., Y. Pan, F. Qi, and P. W. Caufield. 2003. Identification of Streptococcus sanguinis with a PCR-generated species-specific DNA probe. J. Clin. Microbiol. 41:3481-3486.
21. Monstein, H., S. Nikpour-Badr, and J. Jonasson. 2001. Rapid molecular identification and subtyping of Helicobacter pylori by pyrosequencing of the 16S rDNA variable V1 and V3 regions. FEMS Microbiol. Lett. 199:103-107.
22. Picard, F. J., D. Ke, D. K. Boudreau, M. Boissinot, A. Huletsky, D. Richard, M. Ouellette, P. H. Roy, and M. G. Bergeron. 2004. Use of tuf sequences for genus-specific PCR detection and phylogenetic analysis of 28 streptococcal species. J. Clin. Microbiol. 42:3686-3695.
23. Poyart, C., G. Quesne, S. Coulon, P. Berche, and P. Trieu-Cuot. 1998. Identification of streptococci to species level by sequencing the gene encoding the manganese-dependent superoxide dismutase. J. Clin. Microbiol. 36: 41-47.
24. Poyart, C., G. Quesne, and P. Trieu-Cuot. 2002. Taxonomic dissection of the Streptococcus bovis group by analysis of manganese-dependent superoxide dismutase gene (sodA) sequences: reclassification of "Streptococcus infantarius subsp. coli" as Streptococcus lutetiensis sp. nov. and of Streptococcus bovis biotype 11.2 as Streptococcus pasteurianus sp. nov. Int. J. Syst. Evol. Microbiol. 52:1247-1255.
25. Regnault, B., F. Grimont, and P. A. Grimont. 1997. Universal ribotyping method using a chemically labeled oligonucleotide probe mixture. Res. Microbiol. 148:649-659.
26. Ronaghi, M. 2001. Pyrosequencing sheds light on DNA sequencing. Genome Res. 11:3-11.
27. Ronaghi, M., and E. Elahi. 2002. Pyrosequencing for microbial typing. J. Chromatogr. B Anal. Technol. Biomed. Life Sci. 782:67-72.
28. Ronaghi, M., M. Uhlen, and P. Nyren. 1998. A sequencing method based on real-time pyrophosphate. Science 281:363-365.
29. Ruoff, K. L., S. I. Miller, C. V. Garner, M. J. Ferraro, and S. B. Calderwood. 1989. Bacteremia with Streptococcus bovis and Streptococcus salivarius: clinical correlates of more accurate identification of isolates. J. Clin. Microbiol. 27:305-308.
30. Ruoff, K. L., R. Whiley, and D. Beighton. 2003. Streptococcus, p. 405-421. In P. R. Murray, E. J. Baron, M. A. Pfaller, J. H. Jorgensen, and R. H. Yolken (ed.), Manual of clinical microbiology, 8th ed. ASM Press, Washington, DC.
31. Schlegel, L., F. Grimont, E. Ageron, P. A. D. Grimont, and A. Bouvet. 2003. Reappraisal of the taxonomy of the Streptococcus bovis/Streptococcus equinus complex and related species: description of Streptococcus gallolyticus subsp. gallolyticus subsp. nov., S. gallolyticus subsp. macedonicus subsp. nov. and S. gallolyticus subsp. pasteurianus subsp. nov. Int. J. Syst. Evol. Microbiol. 53: 631-645.
32. Schlegel, L., F. Grimont, P. A. D. Grimont, and A. Bouvet. 2003. Identification of major streptococcal species by rrn-ampiified ribosomal DNA restriction analysis. J. Clin. Microbiol. 41:657-666.
33. Seppälä, H., M. Haanperä, M. Al-Juhaish, H. Järvinen, J. Jalava, and P. Huovinen. 2003. Antimicrobial susceptibility patterns and macrolide resistance genes of viridans group streptococci from normal flora. J. Antimicrob. Chemother. 52:636-644.
34. Sinclair, A., C. Arnold, and N. Woodford. 2003. Rapid detection and estimation by pyrosequencing of 23S rRNA genes with a single nucleotide polymorphism conferring linezolid resistance in enterococci. Antimicrob. Agents Chemother. 47:3620-3622.
35. Sly, L. I., M. M. Cahill, R. Osawa, and T. Fujisawa. 1997. The tannin-degrading species Streptococcus gallolyticus and Streptococcus capnnus are subjective synonyms. Int. J. Syst. Bacteriol. 47:893-894.
36. Teng, L. J., P. R. Hsueh, J. C. Tsai, P. W. Chen, J. C. Hsu, H. C. Lai, C. N. Lee, and S. W. Ho. 2002. groESL sequence determination, phylogenetic analysis, and species differentiation for viridans group streptococci. J. Clin. Microbiol. 40:3172-3178.
37. Tapp, J., M. Thollesson, and B. Herrmann. 2003. Phylogenetic relationships and genotyping of the genus Streptococcus by sequence determination of the RNase P RNA gene, rnpB. Int. J. Syst. Evol. Microbiol. 53:1861-1871.